\HeaderA{unWantedComp}{A function to manually remove protein complexes from some in
silico interactome}{unWantedComp}
\keyword{datagen}{unWantedComp}
\begin{Description}\relax
This function takes in an in silico interactome by its bipartite graph
representation and a character vector of complex ID's. The function
parses through the column names of the in silico interactome and
removes those columns whose names are found in the character vector.
\end{Description}
\begin{Usage}
\begin{verbatim}
unWantedComp(ISI, unwantedComplex = c("GO:0000262", "GO:0000228",
"GO:0000775", "GO:0010008", "GO:0005792", "GO:0005768", "GO:0005769",
"GO:0005770", "GO:0005777", "GO:0005844", "GO:0001400"), unwantedGenes =
c("RNA_TLC1", "SNRNA_NME1","RNA_RNASE-P"))
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{ISI}] The in silico interactome as a bipartite graph
\item[\code{unwantedComplex}] A character vector. Each entry is a protein
complex id for which should be removed from the interactome.
\item[\code{unwantedGenes}] A character vector of gene names that will be
deleted from the row indexing set of the in silico interactome.
\end{ldescription}
\end{Arguments}
\begin{Value}
An incidence matrix. A new matrix with those columns indexed by
unwantedComplex removed. It will also remove any protein which is now
no longer contained in any protein complex.
\end{Value}
\begin{Note}\relax
The entries of unwantedComplex must be found in the column names of
ISI, otherwise, they will not be removed. This is especially important
since there are many id's that index the same protein complex.
\end{Note}
\begin{Author}\relax
T. Chiang
\end{Author}
\begin{Examples}
\begin{ExampleCode}

#mips = getMipsInfo()
#go = getGOInfo()
#mipsM = createMipsMatrix(mips)
#goM = createGOMatrix(go)
#mips2go = runCompareComplex(mipsM, goM, byWhich = "ROW")
#merged = mergeBGMat(mipsM, goM, mips2go$toBeRm)
#ISI = unWantedComp(merged)

\end{ExampleCode}
\end{Examples}

